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Room temperature (280K) crystal structure of KAPOSI'S sarcoma- associated herpesvirus protease in complex with allosteric inhibitor (compound 733)
Analyse Room temperature (280K) crystal structure of KAPOSI'S sarcoma- associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V5E
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf 17
- UniProt
- O40922
- Ligands
- 8N4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf 17 | protein | 188 | 30% helix, 27% strand | O40922 |
| B | Orf 17 | protein | 181 | 30% helix, 29% strand | O40922 |
Ligands and binding sites
- 8N4 · 4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-{[3-(trifluoromethoxy)phenyl]amino}benzoic acid · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.73 | 0.78 | 70 | empty |
| 2 | 187 | 0.52 | 0.77 | 21 | 8N4 |
| 3 | 168 | 0.49 | 0.76 | 20 | 8N4 |
| 4 | 56 | 0.24 | 0.71 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 647 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5V5E · Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O40922
- Elsewhere: RCSB PDB 5V5E · PDBe 5V5E · UniProt O40922
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